Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1109788068:

Variant ID: vg1109788068 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 9788068
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTCACGCAGACGAAAGAACACGATATTGAGCATCAAGACTAGATGTTCTTGAGTAACTCGGACACGGCCTTCCAGGACTCGGAGAAGACCAAGCTCTTG[C/T]
GGGTGGTGACGTAGGCCTCGCCGTCGCGCTCGTCACCGAAGACCTCTTTGATCATGTTAATGGCATGGCCCTTCAGCTCCCACTGGTCGTCGCACACTCG

Reverse complement sequence

CGAGTGTGCGACGACCAGTGGGAGCTGAAGGGCCATGCCATTAACATGATCAAAGAGGTCTTCGGTGACGAGCGCGACGGCGAGGCCTACGTCACCACCC[G/A]
CAAGAGCTTGGTCTTCTCCGAGTCCTGGAAGGCCGTGTCCGAGTTACTCAAGAACATCTAGTCTTGATGCTCAATATCGTGTTCTTTCGTCTGCGTGAAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.20% 0.80% 0.02% 0.00% NA
All Indica  2759 98.70% 1.30% 0.04% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 96.80% 3.00% 0.22% 0.00% NA
Indica III  913 98.20% 1.80% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.80% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1109788068 C -> T LOC_Os11g17580.1 missense_variant ; p.Arg216His; MODERATE nonsynonymous_codon ; R216H Average:70.424; most accessible tissue: Callus, score: 85.41 unknown unknown DELETERIOUS 0.00